1. f3d Format for Storage of 3D Grids
Miloš Šrámek
Austrian Academy of Sciences

2. What would be nice... Support for different kinds of voxels
Scalar and color voxels
8, 16, 32 bit integers, signed and unsigned, floats
Different kinds of grids
cartesian
regular
rectilinear

3. What would be nice... Self descriptive
Stores all necessary data attributes
Application specific comments
Provide means to transfer information between different applications
Preview image
An icon image, giving an idea about the contents of the file.
Data compression

4. What would be nice... Cross platform compatibility Little/Big endian
Size of voxel representation
Availability
Covered by a non-restrictive license
Ease of usage

5. 3D Formats and Approaches
Sequence of slices
Preview is possible, otherwise awkward
Raw 3D Data
Easy to use (load), hard to manipulate
Everything else is bad
Package specific formats (AVS, DE, VTK):
Too general (structured/unstructured, geometry, topology, attributes)
Not available outside the package

6. Existing 3D Formats HDF and netCDF Too complicated No preview
DICOM (ACR-NEMA)
Complex, only 2D format, (usually) no compression
ANALYZE
No preview, no compression
ETC...

7. The ‘f3d’ Format A 3D extension of the PNM format
Keeps the basic simple structure of PNM:
Magic (P5, P6)
# Comments
Dimensions (2D)
2D image data (preview)
3D extension
3D data is appended as compressed 2D slices (zlib compression)
Parameters stored as PNM comments

8. Features Preview (data reprojected along an axis)
Any image viewer
Simplifies manipulation with files (what the hell is in this file?)
ASCII header and comments
Viewable by image viewers (xv)
Viewable by vi (can be even edited!)
Compression
Ratio up to 50 for synthetic data or 2 for noisy measured data

9. PNM - f3d Header Comments
Regular PNM comments, e.g.: #
f3d format attributes, e.g.:
#!f3d 1.2
#!vdim
f3d format comments
#!comment File created by 'vxtGrid3D'
Application specific parameters, e.g.:
#!comment vxt density

10. Basic C Library (libf3dformat)
Reading:
f3dReadHeader
f3dReadSlice
f3dReadGrid, f3dReadCubGrid
Writing: analogous
Other:
f3dSetHdrComment, f3dDelHdrComment
f3dHostType
f3dVoxelSize

11. C++ Class Library (libf3dclass)
Basic access to data voxels
File storage and retrieval
3D data processing
filters, segmentation, rendering, interpolation, transformations, gradient, ...
Typeless reading of 3D data

12. f3d Tools f3d functionality implemented in the form of UNIX filters:
f3dprog [sw] [input.f3d] > output.f3d
Filter concatenation is possible: tool1 [sw] in.f3d |...| toolN [sw] > out.f3d
f3dview – simple slice viewer

13. f3d Tools: Format Conversion
Readers: raw data, stack of 8 and 16 bit slices, VTK, DICOM
Example: convert a raw volume with 32 bit voxels to f3d:
raw2f3d -i in.raw -r -l 5 -s > out.f3d
Command usage: f3dcmd -h

14. f3d Tools: Point Operators
f3d2f3d (voxel type conversion), f3dinvert, f3dthresh, f3darith, f3d2rith2, f3dmask
Example: Delete bone from CT data:
f3dthresh -lo 90 in.f3d | f3dmask -i in.f3d > out.f3d

15. f3d Tools: Local Operators (Filters)
Data processing in a local voxel neighborhood
Order filters: f3dmax, f3dmin, f3dmedian
Example: Noise removal by the median filter
f3dmedian -k 3 in.f3d > out.f3d

16. f3d Tools: Local Operators (Filters)
Data processing in a local voxel neighborhood
Order filters: f3dmax, f3dmin, f3dmedian
Example: Noise removal by the median filter
f3dmedian -k 3 in.f3d | f3drender -lo 90 -surfg > out.png

17. f3d Tools: Local Operators Gaussian filtering
Convolution by a Gaussian with different widths
Example (data smoothing):
f3dgauss -w 2 in.f3d > out.f3d

18. f3d Tools: Local Operators Gaussian filtering
Convolution by a Gaussian with different widths
Example (noise removal):
f3dgauss -w 2 in.f3d > out.f3d

19. f3d Tools: Local Operators Gradient Estimation
Convolution by a Gabor filter with different widths
Example :
f3dgabor -x -w 3 in.f3d > out.f3d -x -y -z

20. f3d Tools: Local Operators Gradient Estimation
Convolution by a Gabor with different widths in all 3 directions
Example :
f3dgrad -w 3 in.f3d > out.f3d

21. f3d Tools: Local Operators Gradient Magnitude Estimation
Magnitude of the Gabor filter applied to all 3 directions, edge detection
Example :
f3dgradmag -w 3 in.f3d > out.f3d
-w 1
-w 3
-w 5

22. More about f3d